EpitoCore: Mining Conserved Epitope Vaccine Candidates in the Core Proteome of Multiple Bacteria Strains

Shotgun Immunoproteomic Approach for the Discovery of Linear B-Cell Epitopes in Biothreat Agents Francisella tularensis and Burkholderia pseudomallei

Peptide-based subunit vaccines are coming to the forefront of current vaccine approaches, with safety and cost-effective production among their top advantages. Peptide vaccine formulations consist of multiple synthetic linear epitopes that together trigger desired immune responses that can result in robust immune memory. The advantages of linear compared to conformational epitopes are their simple structure, ease of synthesis, and ability to stimulate immune responses by means that do not require complex 3D conformation. Prediction of linear epitopes through use of computational tools is fast and cost-effective, but typically of low accuracy, necessitating extensive experimentation to verify results. On the other hand, identification of linear epitopes through experimental screening has been an inefficient process that requires thorough characterization of previously identified full-length protein antigens, or laborious techniques involving genetic manipulation of organisms. In this study, we apply a newly developed generalizable screening method that enables efficient identification of B-cell epitopes in the proteomes of pathogenic bacteria. As a test case, we used this method to identify epitopes in the proteome of Francisella tularensis (Ft), a Select Agent with a well-characterized immunoproteome. Our screen identified many peptides that map to known antigens, including verified and predicted outer membrane proteins and extracellular proteins, validating the utility of this approach. We then used the method to identify seroreactive peptides in the less characterized immunoproteome of Select Agent Burkholderia pseudomallei (Bp). This screen revealed known Bp antigens as well as proteins that have not been previously identified as antigens. Although B-cell epitope prediction tools Bepipred 2.0 and iBCE-EL classified many of our seroreactive peptides as epitopes, they did not score them significantly higher than the non-reactive tryptic peptides in our study, nor did they assign higher scores to seroreactive peptides from known Ft or Bp antigens, highlighting the need for experimental data instead of relying on computational epitope predictions alone. The present workflow is easily adaptable to detecting peptide targets relevant to the immune systems of other mammalian species, including humans (depending upon the availability of convalescent sera from patients), and could aid in accelerating the discovery of B-cell epitopes and development of vaccines to counter emerging biological threats.

Proteome-wide analysis of Coxiella burnetii for conserved T-cell epitopes with presentation across multiple host species

Background

Coxiella burnetii is the Gram-negative bacterium responsible for Q fever in humans and coxiellosis in domesticated agricultural animals. Previous vaccination efforts with whole cell inactivated bacteria or surface isolated proteins confer protection but can produce a reactogenic immune responses. Thereby a protective vaccine that does not cause aberrant immune reactions is required. The critical role of T-cell immunity in control of C. burnetii has been made clear, since either CD8⁺ or CD4⁺ T cells can empower clearance. The purpose of this study was to identify C. burnetii proteins bearing epitopes that interact with major histocompatibility complexes (MHC) from multiple host species (human, mouse, and cattle).

Results

Of the annotated 1815 proteins from the Nine Mile Phase I (RSA 493) assembly, 402 proteins were removed from analysis due to a lack of inter-isolate conservation. An additional 391 proteins were eliminated from assessment to avoid potential autoimmune responses due to the presence of host homology. We analyzed the remaining 1022 proteins for their ability to produce peptides that bind MHCI or MHCII. MHCI and MHCII predicted epitopes were filtered and compared between species yielding 777 MHCI epitopes and 453 MHCII epitopes. These epitopes were further examined for presentation by both MHCI and MHCII, and for proteins that contained multiple epitopes. There were 31 epitopes that overlapped positionally between MHCI and MHCII across host species. Of these, there were 9 epitopes represented within proteins containing ≥ 5 total epitopes, where an additional 24 proteins were also epitope dense. In all, 55 proteins were found to contain high scoring T-cell epitopes. Besides the well-studied protein Com1, most identified proteins were novel when compared to previously studied vaccine candidates.

Conclusion

These data represent the first proteome-wide evaluation of C. burnetii peptide epitopes. Furthermore, the inclusion of human, mouse, and bovine data capture a range of hosts for this zoonotic pathogen plus an important model organism. This work provides new vaccine targets for future vaccination efforts and enhances opportunities for selecting multiple T-cell epitope types to include within a vaccine.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-021-04181-w.

Immunity against Lagovirus europaeus and the Impact of the Immunological Studies on Vaccination

In the early 1980s, a highly contagious viral hemorrhagic fever in rabbits (Oryctolagus cuniculus) emerged, causing a very high rate of mortality in these animals. Since the initial occurrence of the rabbit hemorrhagic disease virus (RHDV), several hundred million rabbits have died after infection. The emergence of genetically-different virus variants (RHDV GI.1 and GI.2) indicated the very high variability of RHDV. Moreover, with these variants, the host range broadened to hare species (Lepus). The circulation of RHDV genotypes displays different virulences and a limited induction of cross-protective immunity. Interestingly, juvenile rabbits (<9 weeks of age) with an immature immune system display a general resistance to RHDV GI.1, and a limited resistance to RHDV GI.2 strains, whereas less than 3% of adult rabbits survive an infection by either RHDV GI.1. or GI.2. Several not-yet fully understood phenomena characterize the RHD. A very low infection dose followed by an extremely rapid viral replication could be simplified to the induction of a disseminated intravascular coagulopathy (DIC), a severe loss of lymphocytes—especially T-cells—and death within 36 to 72 h post infection. On the other hand, in animals surviving the infection or after vaccination, very high titers of RHDV-neutralizing antibodies were induced. Several studies have been conducted in order to deepen the knowledge about the virus’ genetics, epidemiology, RHDV-induced pathology, and the anti-RHDV immune responses of rabbits in order to understand the phenomenon of the juvenile resistance to this virus. Moreover, several approaches have been used to produce efficient vaccines in order to prevent an infection with RHDV. In this review, we discuss the current knowledge about anti-RHDV resistance and immunity, RHDV vaccination, and the further need to establish rationally-based RHDV vaccines.